AP Biology Notes Outline
Enduring Understanding 1.B
Big Idea 1:
The process of evolution drives the diversity and unity of life.
Enduring Understanding 1.B:
Organisms are linked by lines of descent from common ancestry.
Learning Objectives:
Essential Knowledge 1.B.1: Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
(1.14) The student is able to pose scientific questions that correctly identify essential properties of shared, core life processes that provide insights into the
history of life on Earth.
(1.15) The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life,
and how these shared, conserved core processes and features support the concept of common ancestry for all organisms.
(1.16) The student is able to justify the scientific claim that organisms share many conserved core processes and features that evolved and are widely
distributed among organisms today.
Essential Knowledge 1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.
(1.17) The student is able to pose scientific questions about a group of organisms whose relatedness is described by a phylogenetic tree or cladogram in order to
(1) identify shared characteristics, (2) make inferences about the evolutionary history of the group, and (3) identify character data that could extend or improve
the phylogenetic tree.
(1.18) The student is able to evaluate evidence provided by a data set in conjunction with a phylogenetic tree or a simple cladogram to determine evolutionary
history and speciation.
(1.19) The student is able to create a phylogenetic tree or simple cladogram that correctly represents evolutionary history and speciation from a provided data
set.
Required Readings:
Textbook Ch. 26
Practicing Biology Homework Questions:
Questions #20-23
Essential Knowledge 1.B.1: Organisms share many conserved core processes and features that evolved and
are widely distributed among organisms today.
Organisms share many conserved core processes and features that are widely distributed among organisms today. These processes
provide evidence that all organisms (Archaea, Bacteria, and Eukarya, both extant and extinct) are linked by lines of descent from
common ancestry. Elements that are conserved across all domains of life are DNA and RNA as carriers of genetic information, a
universal genetic code, and many metabolic pathways. The existence of these properties in organisms today implies that they were
present in a universal ancestor and that present life evolved from a universal ancestor. In eukaryotes, conserved core elements
provide evidence for evolution. These features include the presence of a cytoskeleton, a nucleus, membrane-bound organelles,
linear chromosomes and endomembrane systems.
Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics. Early taxonomists
classified all species as either plants or animals. Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae,
Fungi, and Animalia. More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya. The threedomain system is supported by data from many sequenced genomes.
The Three-Domain System describes classification as:
• Not all prokaryotes are closely related (not monophyletic)
• Prokaryotes split early in the history of living things (not all in one lineage)
• Archaea are more closely related to Eukarya than to Bacteria
• Eukarya are not directly related to Eubacteria
• There was a common ancestor for all extant organisms (monophyletic)
• Eukaryotes are more closely related to each other (than prokaryotes are to each other)
L. Carnes
Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
Structural and functional evidence supports the relatedness of all domains. Illustrative examples include:
1. DNA and RNA are carriers of genetic information through transcription, translation and replication. The organizational basis of
all living systems is heritable information. The proper storage and transfer of this information are critical for life to continue at
the cell, organism, and species level.
• Non-eukaryotic organisms have circular chromosomes; eukaryotic organisms have multiple linear chromosomes. Viruses
have RNA or DNA.
• In all organisms, genetic information flows from a sequence of nucleotides in a gene to a sequence of amino acids in a
protein.
• DNA replication ensures the continuity of hereditary information across all domains.
2.
Major features of the genetic code are shared by all modern living systems. Metabolic pathways are conserved across all
currently recognized domains. A, T, C, G, U are the nitrogenous bases found in all living organisms.
• Replication enzymes ensure that DNA is replicated before being passed to daughter cells.
• Phenotypes are determined through protein activities.
3.
Cell communication processes share common features that reflect a shared evolutionary history. Communication in all
organisms involves transduction of stimulatory or inhibitory signals from other cells, organisms or the environment.
• In single-celled organisms, signal transduction pathways influence how the cell responds to its environment (quorum
sensing; chemotaxis).
• In multi-celled organisms, signal transduction pathways coordinate the activities within individual cells that support the
function of the organism as a whole (temperature determination of sex in vertebrates; epinephrine stimulation of glycogen
breakdown in mammals).
Structural evidence supports the relatedness of all eukaryotes. Illustrative examples include:
1. Cytoskeleton – found in all eukaryotic cells - a network of structural proteins that facilitate cell movement, morphological
integrity and organelle transport found in all eukaryotic cells.
2. Membrane-bound Organelles – found in all eukaryotic cells - membranes & membrane-bound organelles compartmentalize
intracellular metabolic processes and therefore minimize competing interactions. They also facilitate cellular processes by
increasing SA where reactions occur. Smooth & Rough ER, Golgi, Mitochondria & Chloroplasts are an example. Archaea and
bacteria generally lack internal membranes.
3. Endomembrane Systems – found in all eukaryotic cells – the collection of membranes inside and around a cell, related either to
direct physical contact or by the transfer of membranous vesicles; includes the smooth & rough ER, the Golgi apparatus,
lysosomes, and vacuoles.
4. Linear Chromosomes – found in all eukaryotes - easily duplicated and divided to daughter cells – prokaryotes generally have
circular chromosomes.
Essential Knowledge 1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of
evolutionary history that can be tested.
Phylogeny is the evolutionary history of a species or group of species. To construct a phylogeny, biologists utilize systematics, a
discipline focused on classifying organisms and determining their evolutionary relationships. Systematists use data ranging from
fossils to molecules and genes to infer evolutionary relationships. Taxonomy is an ordered division of organisms into categories
based on a set of characteristics used to assess similarities and differences. Phylogenetic trees graphically model evolutionary
history and can represent both acquired traits and those lost during evolution. This information enables biologists to construct a
comprehensive tree of life, which will continue to be refined as additional data are collected.
Each branch point (node) represents the divergence of two species.
Sister taxa are groups that share an immediate common ancestor
Phylogenetic trees and cladograms can represent traits that are either
derived or lost due to evolution. Phylogenetic trees and cladograms
illustrate speciation that has occurred, in that relatedness of any two
groups on the tree is shown by how recently two groups had a
common ancestor.
Phylogenetic trees and cladograms can be constructed from
morphological similarities of living or fossil species, and from DNA and
protein sequence similarities – by employing computer programs that
have sophisticated ways of measuring and representing relatedness among
organisms. Phylogenetic trees and cladograms are dynamic – constantly
being revised based on current and emerging knowledge.
Using phylogenetic trees and cladograms, we can represent traits that are
either derived or lost due to evolution. Illustrative examples include:
• Number of heart chambers in animals (DERIVED)
• Absence of legs in some sea mammals (LOST)
A powerful four-chambered heart was an essential adaptation of the
endothermic way of life characteristic of mammals and birds. The
separation of the systemic and pulmonary circuits, each independently
powered, allows organisms to deliver much more fuel and O 2 to tissues –
because endotherms use about 10 times as much energy as ectotherms.
Fishes have a two-chambered heart and a single circuit of blood flow. Blood leaves heart and
passes through two capillary beds before returning to the heart under reduced pressure. The
heart has two main chambers, one ventricle and one atrium. Blood pumped from the
ventricle travels to the gills, where it picks up O2 and disposes of CO2. This is an example of
SINGLE CIRCULATION – blood passes through the heart once in each complete circuit – blood
flows directly from respiratory organs to other organs, under reduced pressure.
Amphibians have a three-chambered heart and two circuits of blood flow:
pulmocutaneous and systemic.
Reptiles (except birds) have a three-chambered heart, with a septum
partially dividing the single ventricle.
Mammals & birds have a four-chambered heart with a double circulatory system (pulmonary
and systemic). The ventricle is completely divided into separate right and left chambers. The
left side of the heart pumps and receives only oxygen-rich blood while the right side receives
and pumps only oxygen-poor blood. The circulatory systems of frogs, reptiles, birds, and
mammals involves DOUBLE CIRCULATION – two distinct circuits (pulmonary & systemic).
Double circulation provides a vigorous flow of blood to the brain, muscles, and other organs
b/c the heart repressurizes the blood destined for these tissues after it passes the capillary
beds of the lungs or skin.
Fossil records indicate that prior to 50
million years ago, most mammals were
terrestrial.
Recently discovered fossils document
the formation of a new species through
the loss of an ancestral character – hind
limbs. Vestigial structures still remain
(pelvis bone).
To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms. Organisms
with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or
sequences. When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or
analogy:
• Homology is similarity due to shared ancestry – such as the bones of a whale’s flipper and a tiger’s paw.
• Analogy is similarity due to convergent evolution - occurs when similar environmental pressures and natural selection
produce similar (analogous) adaptations in organisms from different evolutionary lineages (example: the streamlined
bodies of a tuna and a dolphin).
• Bat and bird wings are homologous as forelimbs, but analogous as functional wings.
• Homology can be distinguished from analogy by comparing
fossil evidence and the degree of complexity. The more
complex two similar structures are, the more likely it is that
they are homologous.
• Molecular systematics uses DNA and other molecular data to
determine evolutionary relationships. The more alike the DNA
sequences of two organisms, the more closely related they are
evolutionarily.
In comparison with its ancestor, an organism has both shared and different characteristics: an ancestral character is a character
that originated in an ancestor of the taxon. A derived character is an evolutionary novelty unique to a particular clade. Derived
characters are used to construct phylogenetic trees because they infer evolutionary change!
Performing Outgroup Comparisons:
0 = character absent; 1 = character present
When inferring evolutionary relationships, it is useful
to know in which clade a shared derived character
first appeared.
 An outgroup is a species or group of species
that is closely related to the ingroup, the
various species being studied.
 Systematists compare each ingroup species
with the outgroup to differentiate between
shared derived and shared ancestral
characteristics.
 Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups
from a common ancestor…very important!
Systematists can never be sure of finding the best tree in a large data set. They narrow possibilities by applying two important
phylogenetic principles:
1. Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived
characters) is the most likely – i.e. the simplest explanations is generally the correct explanation (Occam’s razor). The most
parsimonious evolutionary trees require the fewest base changes.
2. The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found
that reflects the most likely sequence of evolutionary events.
The best hypotheses for phylogenetic trees fit the most
data: morphological, molecular, and fossil record evidence.
Phylogenetic bracketing allows us to predict features of an
ancestor from features of its descendants.
This has been applied to infer features of dinosaurs from
their descendants: birds and crocodiles.
Evidence suggests that birds descended from theropod dinosaurs. The closest LIVING
relative to birds are crocodiles. Birds and crocodiles share numerous features:
 4 chambered heart, singing to defend territory or attract mate; build nests,
brood care for eggs/warm with body…and all of these features were likely
present in the common ancestor to birds and crocodiles.
 As such, biologists predict that dinosaurs had 4-chambered hearts, sang, built
nests, and exhibited brooding. Fossil evidence supports this prediction!
Taxonomy is flux and constantly changing in the light of new data. The most recently adopted classification for our tree of life is
the three domain system, which includes Bacteria, Archaea, and Eukarya. This system arose from the finding that there are two
distinct lineages of prokaryotes. As we gain more tools for analysis, earlier ideas about evolutionary relatedness are changed, and so
taxonomy, too, continues to evolve.